The Assistant Special Agent in Charge for the president's Secret Service detail believed to be involved in a long-term affair with a Mexican woman committed suicide a day after failing a national security polygraph and being stripped of his clearances and access, according to sources.

Rafael Prieto, a supervisor on President Obama's Secret Service detail, was found dead last weekend in the passenger side seat of his roommate's car in the garage of their Washington D.C. residence, clutching a photograph of his two children, multiple sources told FoxNews.com. The suicide came a day after a Do Not Admit email sent agency-wide for Prieto was sent by the Security Clearance Division.

A senior law enforcement official confirmed Prieto's clearance had been pulled, calling it "standard practice" for an employee going through an "administrative process." The official said the investigation "was related to clarifying a long-term ongoing relationship with a foreign national."

Sources have told FoxNews.com that Prieto was given a polygraph because of an alleged extramarital affair with a Mexican national -- a strict violation of Secret Service policy. The sources said Preito had been carrying on the affair for several years, and said his relationship was well known within the Service. The head of Obama's Secret Service detail, Vic Erevia, had previous knowledge of Prieto's relationship, according to sources.

But Secret Service spokesman Ed Donovan on Friday told FoxNews.com: "It seems ridiculous to expect that a supervisor ... that supervises several hundred employees would have intimate knowledge of each employee's personal home-life situation."

Sources, though, have told FoxNews.com that Prieto had brought the woman to Secret Service functions attended by Secret Service supervisors. Among the events she attended was a party for Dennis Martinez-Ramos, then the head of the Orlando field office, at a suburban Washington-area cigar bar earlier this year. According to multiple sources who attended, Erevia was also at that party.

Sources said Prieto's relationship with the Mexican woman earlier this year came to the attention of the Department of Homeland Security's Office of Inspector General (DHS OIG), which is conducting multiple investigations into the Secret Service in the wake of the Cartagena, Colombia prostitution scandal. The pressure of the ongoing DHS OIG investigations led Secret Service to finally -- after what sources say were years of turning a blind eye to Prieto's relationship -- bring him in to be questioned late last week.

Prieto was married and is survived by two children, who live in New York with their mother, sources said. Prieto had been living with the roommate in Washington, sources said.